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- PDB-8f6c: E. coli cytochrome bo3 ubiquinol oxidase dimer -

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Basic information

Entry
Database: PDB / ID: 8f6c
TitleE. coli cytochrome bo3 ubiquinol oxidase dimer
Components(Cytochrome bo(3) ubiquinol oxidase subunit ...) x 4
KeywordsPROTON TRANSPORT / heme-copper oxidase / proton translocation / E. coli aerobic respiratory chain / membrane protein / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity ...oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane
Similarity search - Function
: / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II ...: / Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase subunit IV / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / Cytochrome C oxidase subunit IV, prokaryotes / COX aromatic rich motif / Prokaryotic Cytochrome C oxidase subunit IV / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Helix Hairpins - #90 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Helix Hairpins / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / HEME O / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome bo(3) ubiquinol oxidase subunit 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsGuo, Y. / Karimullina, E. / Borek, D. / Savchenko, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci / Year: 2023
Title: Monomer and dimer structures of cytochrome bo ubiquinol oxidase from Escherichia coli.
Authors: Yirui Guo / Elina Karimullina / Tabitha Emde / Zbyszek Otwinowski / Dominika Borek / Alexei Savchenko /
Abstract: The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it ...The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts-the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74).
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
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Revision 1.1Dec 14, 2022Group: Refinement description / Category: refine / Item: _refine.ls_d_res_high
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome bo(3) ubiquinol oxidase subunit 1
B: Cytochrome bo(3) ubiquinol oxidase subunit 2
C: Cytochrome bo(3) ubiquinol oxidase subunit 3
D: Cytochrome bo(3) ubiquinol oxidase subunit 4
E: Cytochrome bo(3) ubiquinol oxidase subunit 1
F: Cytochrome bo(3) ubiquinol oxidase subunit 2
G: Cytochrome bo(3) ubiquinol oxidase subunit 3
H: Cytochrome bo(3) ubiquinol oxidase subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,41120
Polymers267,8858
Non-polymers7,52612
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

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Cytochrome bo(3) ubiquinol oxidase subunit ... , 4 types, 8 molecules AEBFCGDH

#1: Protein Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome b562-o complex subunit I / Cytochrome o ubiquinol oxidase subunit 1 / Cytochrome o ...Cytochrome b562-o complex subunit I / Cytochrome o ubiquinol oxidase subunit 1 / Cytochrome o subunit 1 / Oxidase bo(3) subunit 1 / Ubiquinol oxidase chain A / Ubiquinol oxidase polypeptide I / Ubiquinol oxidase subunit 1


Mass: 73896.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoB, b0431, JW0421 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABI8, ubiquinol oxidase (H+-transporting)
#2: Protein Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome b562-o complex subunit II / Cytochrome o ubiquinol oxidase subunit 2 / Cytochrome o ...Cytochrome b562-o complex subunit II / Cytochrome o ubiquinol oxidase subunit 2 / Cytochrome o subunit 2 / Oxidase bo(3) subunit 2 / Ubiquinol oxidase chain B / Ubiquinol oxidase polypeptide II / Ubiquinol oxidase subunit 2


Mass: 28839.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoA, b0432, JW0422 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ1
#3: Protein Cytochrome bo(3) ubiquinol oxidase subunit 3 / Cytochrome o ubiquinol oxidase subunit 3 / Cytochrome o subunit 3 / Oxidase bo(3) subunit 3 / ...Cytochrome o ubiquinol oxidase subunit 3 / Cytochrome o subunit 3 / Oxidase bo(3) subunit 3 / Ubiquinol oxidase chain C / Ubiquinol oxidase polypeptide III / Ubiquinol oxidase subunit 3


Mass: 20464.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoC, b0430, JW0420 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ3
#4: Protein Cytochrome bo(3) ubiquinol oxidase subunit 4 / Cytochrome o ubiquinol oxidase subunit 4 / Cytochrome o subunit 4 / Oxidase bo(3) subunit 4 / ...Cytochrome o ubiquinol oxidase subunit 4 / Cytochrome o subunit 4 / Oxidase bo(3) subunit 4 / Ubiquinol oxidase chain D / Ubiquinol oxidase polypeptide IV / Ubiquinol oxidase subunit 4


Mass: 10742.083 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoD, b0429, JW0419 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABJ6

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Non-polymers , 4 types, 12 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HEO / HEME O


Mass: 838.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H58FeN4O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli Cytochrome bo3 ubiquinol oxidase dimer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40700 / Symmetry type: POINT
RefinementResolution: 3.46→146.78 Å / Cor.coef. Fo:Fc: 0.734 / SU B: 52.565 / SU ML: 0.717 / ESU R: 1.439
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.43284 --
obs0.43284 98815 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 29.98 Å2
Refinement stepCycle: 1 / Total: 19344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0040.01319958
ELECTRON MICROSCOPYr_bond_other_d0.0290.01619112
ELECTRON MICROSCOPYr_angle_refined_deg1.3881.6427182
ELECTRON MICROSCOPYr_angle_other_deg1.2041.57143794
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.76552388
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.51922.08798
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.793153060
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.9621554
ELECTRON MICROSCOPYr_chiral_restr0.0780.22584
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0221950
ELECTRON MICROSCOPYr_gen_planes_other0.0040.024800
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.0343.2239576
ELECTRON MICROSCOPYr_mcbond_other0.0343.2239574
ELECTRON MICROSCOPYr_mcangle_it0.0664.83411956
ELECTRON MICROSCOPYr_mcangle_other0.0664.83411956
ELECTRON MICROSCOPYr_scbond_it0.013.21810382
ELECTRON MICROSCOPYr_scbond_other0.013.21810383
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other0.0284.82515227
ELECTRON MICROSCOPYr_long_range_B_refined0.51160.1981778
ELECTRON MICROSCOPYr_long_range_B_other0.51160.18981779
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A451940
12E451940
21B160860
22F160860
31C124460
32G124460
41D60500.04
42H60500.04
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.763 7349 -
obs--100 %

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